Thread: [Apbs-users] absolute binding free energy
Biomolecular electrostatics software
Brought to you by:
sobolevnrm
From: 有盼 缪 <you...@ya...> - 2008-12-28 03:53:59
|
Dear , I use GROMACS to study a complex and I want to get the absolute binding free energy of the ligand binding to the protein. In the APBS's Documentation, there are several examples to do with the binding energy, but they are different greatly, so how should I compute the binding free energy? Thank you, youpan ___________________________________________________________ 好玩贺卡等你发,邮箱贺卡全新上线! http://card.mail.cn.yahoo.com/ |
From: Nathan B. <ba...@bi...> - 2008-12-28 22:39:54
|
Hello -- I would not recommend using implicit solvent models to calculate absolute binding free energies; they are best suited to the calculation of relative binding free energies. In fact, the calculation of absolute binding free energy is challenging with nearly any computational method currently available. Can you pose your problem as a relative binding free energy calculation instead? Thanks, Nathan 2008/12/27 有盼 缪 <you...@ya...> > Dear , > > I use GROMACS to study a complex and I want to get the absolute binding > free energy of the ligand binding to the protein. In the APBS's > Documentation, there are several examples to do with the binding energy, but > they are different greatly, so how should I compute the binding free energy? > > Thank you, > youpan > > ------------------------------ > 好玩贺卡等你发,邮箱贺卡全新上线!<http://cn.rd.yahoo.com/mail_cn/tagline/card/*http://card.mail.cn.yahoo.com/> > > ------------------------------------------------------------------------------ > > _______________________________________________ > apbs-users mailing list > apb...@li... > https://lists.sourceforge.net/lists/listinfo/apbs-users > > -- Associate Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ |
From: 有盼 缪 <you...@ya...> - 2008-12-29 15:09:16
|
Hello everyone, If I want to get the relative binding free energy of the ligand--protein complex, what should I do to use the APBS to compute it? Thank you, youpan --- 08年12月29日,周一, Nathan Baker <ba...@bi...> 写道: 发件人: Nathan Baker <ba...@bi...> 主题: Re: [Apbs-users] absolute binding free energy 收件人: you...@ya... 抄送: "apbs apbs" <apb...@li...> 日期: 2008,1229,周一,6:39上午 Hello -- I would not recommend using implicit solvent models to calculate absolute binding free energies; they are best suited to the calculation of relative binding free energies. In fact, the calculation of absolute binding free energy is challenging with nearly any computational method currently available. Can you pose your problem as a relative binding free energy calculation instead? Thanks, Nathan 2008/12/27 有盼 缪 <you...@ya...> Dear , I use GROMACS to study a complex and I want to get the absolute binding free energy of the ligand binding to the protein. In the APBS's Documentation, there are several examples to do with the binding energy, but they are different greatly, so how should I compute the binding free energy? Thank you, youpan 好玩贺卡等你发,邮箱贺卡全新上线! ------------------------------------------------------------------------------ _______________________________________________ apbs-users mailing list apb...@li... https://lists.sourceforge.net/lists/listinfo/apbs-users -- Associate Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ ___________________________________________________________ 好玩贺卡等你发,邮箱贺卡全新上线! http://card.mail.cn.yahoo.com/ |
From: Nathan B. <ba...@bi...> - 2008-12-30 02:06:09
|
Hello -- What sort of relative binding free energy do you want to calculate? An example of relative binding energies calculated with respect to different monovalent ion concentrations is available here: http://apbs.wustl.edu/MediaWiki/index.php/Ionic_strength_dependence_of_peptide-RNA_interactions -- Nathan 2008/12/29 有盼 缪 <you...@ya...> > Hello everyone, > > If I want to get the relative binding free energy of the ligand--protein > complex, what should I do to use the APBS to compute it? > > Thank you, > youpan > > --- *08年12月29日,周一, Nathan Baker <ba...@bi...>* 写道: > > 发件人: Nathan Baker <ba...@bi...> > 主题: Re: [Apbs-users] absolute binding free energy > 收件人: you...@ya... > 抄送: "apbs apbs" <apb...@li...> > 日期: 2008,1229,周一,6:39上午 > > Hello -- > > I would not recommend using implicit solvent models to calculate absolute > binding free energies; they are best suited to the calculation of relative > binding free energies. In fact, the calculation of absolute binding free > energy is challenging with nearly any computational method currently > available. > > Can you pose your problem as a relative binding free energy calculation > instead? > > Thanks, > > Nathan > > 2008/12/27 有盼 缪 <you...@ya...> > >> Dear , >> >> I use GROMACS to study a complex and I want to get the absolute binding >> free energy of the ligand binding to the protein. In the APBS's >> Documentation, there are several examples to do with the binding energy, but >> they are different greatly, so how should I compute the binding free energy? >> >> Thank you, >> youpan >> >> ------------------------------ >> 好玩贺卡等你发,邮箱贺卡全新上线!<http://cn.rd.yahoo.com/mail_cn/tagline/card/*http://card.mail.cn.yahoo.com/> >> >> ------------------------------------------------------------------------------ >> >> _______________________________________________ >> apbs-users mailing list >> apb...@li... >> https://lists.sourceforge.net/lists/listinfo/apbs-users >> >> > > > -- > Associate Professor, Dept. of Biochemistry and Molecular Biophysics > Center for Computational Biology, Washington University in St. Louis > Web: http://cholla.wustl.edu/ > > > ------------------------------ > 好玩贺卡等你发,邮箱贺卡全新上线!<http://cn.rd.yahoo.com/mail_cn/tagline/card/*http://card.mail.cn.yahoo.com/> -- Associate Professor, Dept. of Biochemistry and Molecular Biophysics Center for Computational Biology, Washington University in St. Louis Web: http://cholla.wustl.edu/ |